Solvate with OpenMM

[mattwthompson]

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[codecov]

Codecov Report

❌ Patch coverage is 23.91304% with 35 lines in your changes missing coverage. Please review.
✅ Project coverage is 94.53%. Comparing base (5fce839) to head (7c3a7a8).
⚠️ Report is 3 commits behind head on main.

Files with missing lines	Patch %	Lines
src/pontibus/utils/system_solvation.py	23.91%	35 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #131      +/-   ##
==========================================
- Coverage   95.46%   94.53%   -0.93%     
==========================================
  Files          34       34              
  Lines        2732     2801      +69     
==========================================
+ Hits         2608     2648      +40     
- Misses        124      153      +29     

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[mattwthompson]

This is the only place I can find interchange_packmol_creation imported, so I think that this alias forces the OpenMM code path to be used everywhere in tests

$ grep -r interchange_creation_via_openmm src
src/pontibus/utils/system_creation.py:def interchange_creation_via_openmm(
src/pontibus/protocols/relative/hybridtop_units.py:    interchange_creation_via_openmm as interchange_packmol_creation,

[mattwthompson]

Worked around this one

FAILED src/pontibus/tests/protocols/relative/test_protocol.py::test_dry_run_ligand - assert 2326 == 2278
 +  where 2326 = len({12: 0, 13: 1, 14: 2, 15: 3, ...})
 +    where {12: 0, 13: 1, 14: 2, 15: 3, ...} = <openfe.protocols.openmm_rfe._rfe_utils.relative.HybridTopologyFactory object at 0x7f7873725d10>._env_old_to_new_map
 +      where <openfe.protocols.openmm_rfe._rfe_utils.relative.HybridTopologyFactory object at 0x7f7873725d10> = <instance of HybridRepexSampler>._hybrid_factory

but not sure what to think of

FAILED src/pontibus/tests/utils/test_interchange_packmol.py::test_split_combine_parameters - AssertionError: assert '[#6X4:1]_DUPLICATE' in ['[#1:1]', '[#1:1]-[#6X4]', '[#1:1]-[#6X4]-[#7,#8,#9,#16,#17,#35]', '[#1:1]-[#6X4](-[#7,#8,#9,#16,#17,#35])-[#7,#8,#9,#16,#17,#35]', '[#1:1]-[#6X4](-[#7,#8,#9,#16,#17,#35])(-[#7,#8,#9,#16,#17,#35])-[#7,#8,#9,#16,#17,#35]', '[#1:1]-[#6X4]~[*+1,*+2]', ...]
 +  where '[#6X4:1]_DUPLICATE' = PotentialKey associated with handler 'vdW' with id '[#6X4:1]_DUPLICATE'.id

[mattwthompson]

This is far from a complete, polished work but I think it's in a state which would benefit from some feedback (@IAlibay is surely the most knowledgeable)

• Is the above test failure concerning? It's not part of a code path I intended to change
• Is this generally the right path to be going down?
• What's missing before we can try some runs?

[IAlibay]

This is far from a complete, polished work but I think it's in a state which would benefit from some feedback (@IAlibay is surely the most knowledgeable)

• Is the above test failure concerning? It's not part of a code path I intended to change
• Is this generally the right path to be going down?
• What's missing before we can try some runs?

Thanks, I'll try to review next week.

[IAlibay]

@mattwthompson there's a few things that would be faster done if I can PR into this PR. How much of a pain would it be to move this branch from a fork to this repo directly?

[mattwthompson]

#140